This document provides an overview of reconstructing and using phylogenies. It discusses how phylogenetic trees depict the evolutionary relationships among organisms and are reconstructed from homologous traits. Molecular data like DNA sequences are now most widely used. Phylogenetic analysis allows biologists to make inferences about ancestral traits and timelines of divergence. Molecular clocks also aid in dating evolutionary events. Phylogenetic trees form the basis of biological classification and allow biology to make predictive comparisons across species.

1. Reconstructing and
Using Phylogenies
16

2. Chapter 16 Reconstructing and Using Phylogenies
Key Concepts
• 16.1 All of Life Is Connected through Its
Evolutionary History
• 16.2 Phylogeny Can Be Reconstructed
from Traits of Organisms
• 16.3 Phylogeny Makes Biology
Comparative and Predictive
• 16.4 Phylogeny Is the Basis of Biological
Classification

3. Chapter 16 Opening Question
How are phylogenetic methods used to
resurrect protein sequences from extinct
organisms?

4. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
All of life is related through a common
ancestor:
Phylogeny—the evolutionary history of
these relationships
Phylogenetic tree—a diagrammatic
reconstruction of that history

5. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
A lineage is a series of ancestor and
descendant populations, shown as a line
drawn on a time axis:

6. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
When a single lineage divides into two, it is
depicted as a split or node:

7. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Each descendant population gives rise to a
new lineage, which continues to evolve:

8. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
A phylogenetic tree may portray the
evolutionary history of:
• All life forms
• Major evolutionary groups
• Small groups of closely related species
• Individuals
• Populations
• Genes

9. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
The common ancestor of all the organisms
in the tree forms the root of the tree.

10. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
The splits represent events where one
lineage diverged into two, such as:
• A speciation event (for a tree of species)
• A gene duplication event (for a tree of
genes)
• A transmission event (for a tree of viral
lineages transmitted through a host
population)

11. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Vertical distances between branches don’t
have any meaning, and the vertical order
of lineages is arbitrary.

12. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Taxon—any group of species that we
designate with a name
Clade—taxon that consists of all the
evolutionary descendants of a common
ancestor
Identify a clade by picking any point on the
tree and tracing all the descendant
lineages.

13. Figure 16.1 Clades Represent All the Descendants of a Common Ancestor

14. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Sister species: Two species that are each
other’s closest relatives
Sister clades: Any two clades that are each
other’s closest relatives

15. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Before the 1980s, phylogenetic trees were
used mostly in evolutionary biology, and in
systematics—the study and classification
of biodiversity.
Today trees are widely used in molecular
biology, biomedicine, physiology, behavior,
ecology, and virtually all other fields of
biology.

16. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Evolutionary relationships among species
form the basis for biological classification.
As new species are discovered,
phylogenetic analyses are reviewed and
revised.
The tree of life’s evolutionary framework
allows us to make predictions about the
behavior, ecology, physiology, genetics,
and morphology of species.

17. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Homologous features:
• Shared by two or more species
• Inherited from a common ancestor
They can be any heritable traits, including
DNA sequences, protein structures,
anatomical structures, and behavior
patterns.

18. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Each character of an organism evolves from
one condition (the ancestral trait) to
another condition (the derived trait).
Shared derived traits provide evidence of
the common ancestry of a group and are
called synapomorphies.
The vertebral column is a synapomorphy of
the vertebrates. The ancestral trait was an
undivided supporting rod.

19. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
Similar traits can develop in unrelated
groups:
Convergent evolution—when superficially
similar traits may evolve independently in
different lineages

20. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
In an evolutionary reversal, a character
may revert from a derived state back to an
ancestral state.
These two types of traits are called
homoplastic traits, or homoplasies.

21. Figure 16.2 The Bones Are Homologous, the Wings Are Not

22. Concept 16.1 All of Life Is Connected through Its Evolutionary
History
A trait may be ancestral or derived,
depending on the point of reference.
Example:
• Feathers are an ancestral trait for modern
birds. But in a phylogeny of all living
vertebrates, they are a derived trait found
only in birds.

23. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Ingroup—the group of organisms of primary
interest
Outgroup—species or group known to be
closely related to, but phylogenetically
outside, the group of interest

24. Table 16.1 Eight Vertebrates and the Presence or Absence of Some Shared Derived Traits

25. Figure 16.3 Inferring a Phylogenetic Tree

26. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Parsimony principle—the preferred
explanation of observed data is the
simplest explanation
In phylogenies, this entails minimizing the
number of evolutionary changes that need
to be assumed over all characters in all
groups.
The best hypothesis is one that requires the
fewest homoplasies.

27. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Any trait that is genetically determined can
be used in a phylogenetic analysis.
Morphology—presence, size, shape, or
other attributes of body parts
Phylogenies of most extinct species depend
almost exclusively on morphology.
Fossils provide evidence that helps
distinguish ancestral from derived traits.
The fossil record can also reveal when
lineages diverged.

28. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Limitations of using morphology:
• Some taxa show few morphological
differences
• It is difficult to compare distantly related
species
• Some morphological variation is caused by
environment

29. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Development:
Similarities in developmental patterns may
reveal evolutionary relationships.
Example:
• The larvae of sea squirts has a
notochord, which is also present in all
vertebrates.

30. Figure 16.4 The Chordate Connection (Part 1)

31. Figure 16.4 The Chordate Connection (Part 2)

32. Figure 16.4 The Chordate Connection (Part 3)

33. Figure 16.4 The Chordate Connection (Part 4)

34. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Behavior:
Some traits are cultural or learned, and may
not reflect evolutionary relationships (e.g.
bird songs).
Other traits have a genetic basis and can be
used in phylogenies (e.g. frog calls).

35. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Molecular data:
DNA sequences have become the most
widely used data for constructing
phylogenetic trees.
Nuclear, chloroplast, and mitochondrial DNA
sequences are used.
Information on gene products (such as
amino acid sequences of proteins) are
also used.

36. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Mathematical models are now used to
describe DNA changes over time.
Models can account for multiple changes at
a given sequence position, and different
rates of change at different positions.
Maximum likelihood methods identify the
tree that most likely produced the
observed data. They incorporate more
information about evolutionary change
than do parsimony methods.

37. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of
Organisms
Phylogenetic trees can be tested with
computer simulations and by experiments
on living organisms.
These studies have confirmed the accuracy
of phylogenetic methods and have been
used to refine those methods and extend
them to new applications.

38. Figure 16.5 The Accuracy of Phylogenetic Analysis (Part 1)

39. Figure 16.5 The Accuracy of Phylogenetic Analysis (Part 2)

40. Concept 16.3 Phylogeny Makes Biology Comparative and
Predictive
Applications of phylogenetic trees
• Phylogeny can clarify the origin and
evolution of traits that help in
understanding fundamental biological
processes. This information is then widely
applied in life sciences fields, including
agriculture and medicine.

41. Concept 16.3 Phylogeny Makes Biology Comparative and
Predictive
Self-compatibility:
• Most flowering plants reproduce by mating
with another individual (outcrossing)
Self-incompatible species have mechanisms
to prevent self-fertilization.
Other plants are selfing, which requires that
they be self-compatible.
The evolution of angiosperm fertilization
mechanisms was examined in the genus
Leptosiphon.

42. Figure 16.6 A Portion of the Leptosiphon Phylogeny

43. Concept 16.3 Phylogeny Makes Biology Comparative and
Predictive
Zoonotic diseases:
• Caused by infectious organisms
transmitted from an animal of a different
species (e.g. rabies, AIDS)
Phylogenetic analyses help determine
when, where, and how a disease first
entered a human population.
One example is Human Immunodeficiency
Virus (HIV).

44. Figure 16.7 Phylogenetic Tree of Immunodeficiency Viruses

45. Concept 16.3 Phylogeny Makes Biology Comparative and
Predictive
Evolution of complex traits:
Some adaptations relate to mating behavior
and sexual selection.
One example is the tail of male swordfish.
Phylogenetic analysis supported the
sensory exploitation hypothesis—female
swordtails had a preexisting bias for males
with long tails.

46. Figure 16.8 The Origin of a Sexually Selected Trait

47. Concept 16.3 Phylogeny Makes Biology Comparative and
Predictive
Reconstructing ancestral traits:
• Morphology, behavior, or nucleotide and
amino acid sequences of ancestral
species
Example:
• Opsin proteins (pigments involved in
vision) were reconstructed in the ancestral
archosaur, and it was inferred that it was
probably active at night.

48. Concept 16.3 Phylogeny Makes Biology Comparative and
Predictive
Molecular clocks:
The molecular clock hypothesis states that
rates of molecular change are constant
enough to predict the timing of lineage splits.
A molecular clock uses the average rate at
which a given gene or protein accumulates
changes to gauge the time of divergence .
They must be calibrated using independent
data—the fossil record, known times of
divergence, or biogeographic dates.

49. Figure 16.9 A Molecular Clock of the Protein Hemoglobin

50. Concept 16.3 Phylogeny Makes Biology Comparative and
Predictive
A molecular clock was used to estimate the
time when HIV-1 first entered human
populations from chimpanzees.
The clock was calibrated using the samples
from the 1980s and 1990s, then tested
using the samples from the 1950s.
The common ancestor of this group of HIV-1
viruses can also be determined, with an
estimated date of origin of about 1930.

51. Figure 16.10 Dating the Origin of HIV-1 in Human Populations (Part 1)

52. Figure 16.10 Dating the Origin of HIV-1 in Human Populations (Part 2)

53. Concept 16.4 Phylogeny Is the Basis of Biological Classification
The biological classification system was started
by Swedish biologist Carolus Linnaeus in the
1700s.
Binomial nomenclature gives every species a
unique name consisting of two parts: the genus
to which it belongs, and the species name.
Example:
• Homo sapiens Linnaeus (Linnaeus is the
person who first proposed the name)

54. Concept 16.4 Phylogeny Is the Basis of Biological Classification
Species and genera are further grouped into a
hierarchical system of higher categories such as
family—the taxon above genus.
Examples:
• The family Hominidae contains humans, plus our
recent fossil relatives, plus our closest living
relatives, the chimpanzees and gorillas.
• Rosaceae is the family that includes the genus
Rosa (roses) and its relatives.

55. Concept 16.4 Phylogeny Is the Basis of Biological Classification
Families are grouped into orders
Orders into classes
Classes into phyla (singular phylum)
Phyla into kingdoms
The ranking of taxa within the Linnaean
classification is subjective.

56. Concept 16.4 Phylogeny Is the Basis of Biological Classification
Linnaeus recognized the hierarchy of life,
but he developed his system before
evolutionary thought had become
widespread.
Today, biological classifications express the
evolutionary relationships of organisms.

57. Concept 16.4 Phylogeny Is the Basis of Biological Classification
But detailed phylogenetic information is not
always available.
Taxa are monophyletic—they contain an
ancestor and all descendants of that
ancestor, and no other organisms
(=clade).

58. Concept 16.4 Phylogeny Is the Basis of Biological Classification
Polyphyletic—a group that does not
include its common ancestor
Paraphyletic—a group that does not
include all the descendants of a common
ancestor

59. Figure 16.11 Monophyletic, Polyphyletic, and Paraphyletic Groups

60. Concept 16.4 Phylogeny Is the Basis of Biological Classification
Codes of biological nomenclature:
Biologists around the world follow rules for
the use of scientific names, to facilitate
communication and dialogue.
There may be many common names for one
organism, or the same common name may
refer to several species. But there is only
one correct scientific name.

61. Figure 16.12 Same Common Name, Not the Same Species

62. Answer to Opening Question
Biologists can reconstruct DNA and protein
sequences of a clade’s ancestors if there is
enough information about the genomes of their
descendants.
Real proteins that correspond to proteins in long-
extinct species can be reconstructed.
Mathematical models that incorporate rates of
replacement among different amino acid
residues, substitution rates among nucleotides,
and changes in the rate of molecular evolution
among different lineages, are used.

63. Figure 16.13 Evolution of Fluorescent Proteins of Corals